The thousands of photos and hundreds of illustrations place the Star Trek universe at your fingertips, Planets and stars, weapons and ships, people and places are just part of the meticulous research and the countless cross-references that fill this book.

Articles generally comprise one or two paragraphs. Some contain behind-the-scenes information, annotated in italicized fonts to distinguish them from the in-universe approach of the work. Many also featured images created specifically for the Encyclopedia, including shots of barely visible starships like the Saber-class and Norway-class vessels, and a photograph of Cochrane's statue.

The third edition of the Encyclopedia retained the full-color format, and had both hardcover and softcover releases. However, this edition took a different approach to its update – which covered Star Trek: Insurrection, Deep Space Nine to partway through season 7 (but with main character details covering the final episodes) and Voyager to partway through season 5 – as it was provided in a 128-page appendix to the second edition material. This was a cost-saving measure, as integrating this information alphabetically into the existing material of the second edition would have resulted in a greater publishing expense and thus a higher price. This edition was released in hardcover in Japanese and Italian (translated from English by Massimiliano Antonioli for Fanucci Editore as the Enciclopedia ufficiale di Star Trek). Both of these editions contained fifty pages of additional material over their English-language source publication.

The Encyclopedia was essentially a byproduct from the extensive research the authors had already performed for the Star Trek Chronology, the first edition of which was published one year prior to that of the Encyclopedia. "We again worked by episode, but used the scripts as a reference tool (once they were matched to the aired version of the episode). We catalogued terms, not just chronological data. We did the chronology for the sake of the chronology...it was only afterwards that the idea for the encyclopedia came up.", Co-author Debbie Mirek clarified. [2]

As with its progenitor, not taken into account were officially licensed non-live action works – such as the various Star Treknovels, comics, and games, which are considered apocryphal; nor was Star Trek: The Animated Series, which was considered non-canon at the time of writing the Encyclopedia, or any previously licensed in-universe reference work which had hitherto been considered "official". Mirek commented, regarding the Animated Series: "I am not really sure why it was discounted. I believe Roddenberry did not like the animated series, and Michael, who respected the man enormously, valued his opinion. Gene was largely out of the loop for TNG, in my opinion, so what happened with Star Trek II: The Wrath of Khan and onward, shouldn't be attributed to him. Mike worked on all those films, and they have to be recognized as part of the "universe"." [3]

As of 2002, the official Star Trek franchise treats both the Chronology and the Encyclopedia as the sole primary reference sources (beyond the episodes/movies themselves) for all subsequent in-universe reference works; as such these two works are elevated to the status of "quasi-canon". Licensed works of this kind – such as the later GE Fabbri and Haynes PublishingStar Trek publications (the Okuda author couple are not seldomly assigned to the later publications as "technical consultants" to ensure compliance) – are required to be in concordance with the information contained within these two works. As a consequence, all previous reference works written from an in-universe perspective were no longer considered official references – most notably Franz Joseph's Star Fleet Technical Manual as well as Shane Johnson's Mr. Scott's Guide to the Enterprise and Worlds of the Federation – and no information from these was taken into account in either the Encyclopedia or the Chronology. Labeled "unofficial", these works were de facto debunked and demoted by the franchise to the apocryphal status of novels, comics, and games. (Star Trek: The Magazine Volume 2, Issue 11, p. 71) Greg Jein's "The Case of Jonathan Doe Starship" article, written as a fan two decades earlier, was the only unofficial source acknowledged in the Encyclopedia (1994, p. 57; 1999, pp. 85-86). The Constitution-class registries in the Encyclopedia are largely based on this article, starting their journey to elevation into canon.

Though for the most part adhering to what was canonically established, there was some conjecture included in the Encyclopedia, aside from some of the Constitution-class registries, as the authors made several references to material that was never explicitly noted in canon (i.e. made up exclusively for the Encyclopedia) or that came from unspecified materials that have yet to be identified on screen. The vast majority of these references were the registries, class designations, and some of the classes themselves assigned to Federation starships which were identified on screen by name only, be it orally or visually. Classes noted as conjectural are listed below.

While the authors had incorporated some conjectural historical information in their earlier Chronology, mostly pertaining to early non-canonically established Star Trek history, they refrained from including most of that information in the Encyclopedia, strictly adhering to what was established on screen. However, there were two noticeable exceptions; the designs of the SS Valiant and the Daedalus-class of which Jein had built reference models for representation in the Chronology. Both were also visually represented in the Encyclopedia, as Okuda and Drexler championed their elevation into canon, that of the Daedalus-class in particular. The latter at least managed to make on-screen appearances as a display model, though the link between class-name and appearance remained unestablished. See: Daedalus class model for further information.

The wikia's Memory Alpha site was not used for research when compiling the 2016 edition. [4]